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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ), 'gf_id' => 'HOM05D001631', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001631' ), 'data_identifier' => 'HOM05D001631', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001631', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '395', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p28360' => 'bna', 'A04p28370' => 'bna', 'A05p08750' => 'bna', 'A07p11700' => 'bna', 'A08p26170' => 'bna', 'A09p38450' => 'bna', 'Aa31LG5G22330' => 'aar', 'Aa31LG7G10100' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.1209' => 'aag', 'Actinidia10256' => 'ach', 'Actinidia13322' => 'ach', 'Actinidia19267' => 'ach', 'Actinidia31234' => 'ach', 'Ah.05g166770' => 'amhyb', 'Ah.08g211900' => 'amhyb', 'Ah.10g035070' => 'amhyb', 'Ah.15g092150' => 'amhyb', 'Ah.16g105550' => 'amhyb', 'AL1G41040' => 'aly', 'AL1G41140' => 'aly', 'AL4G33440' => 'aly', 'Aqoxy4G03216' => 'aox', 'Aqoxy6G00613' => 'aox', 'Aqoxy7G01532' => 'aox', 'arahy.Tifrunner.gnm1.ann1.47GAY4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AZN3DT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B10GYL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FDEL0C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HA7VEA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYBJ37' => 'arhy', 'AT1G27600' => 'ath', 'AT2G37090' => 'ath', 'ATR0315G049' => 'atr', 'ATR0767G020' => 'atr', 'ATR1159G034' => 'atr', 'Atru.chr13.927' => 'acertr', 'Atru.chr7.2134' => 'acertr', 'Atru.chr8.2565' => 'acertr', 'AUR62009304' => 'cqu', 'AUR62033829' => 'cqu', 'AUR62035753' => 'cqu', 'AUR62040038' => 'cqu', 'AUR62041719' => 'cqu', 'AUR62041779' => 'cqu', 'BcaB02g09304' => 'bca', 'BcaB03g13979' => 'bca', 'BcaC01g01587' => 'bca', 'BcaC01g06939' => 'bca', 'BcaC02g11835' => 'bca', 'BcaC05g26756' => 'bca', 'BcaC06g35301' => 'bca', 'BcaNung02495' => 'bca', 'BolC3t19691H' => 'bol', 'BolC4t22679H' => 'bol', 'BolC4t28066H' => 'bol', 'BolC7t42273H' => 'bol', 'BraA05t19843Z' => 'bra', 'BraA07t28955Z' => 'bra', 'BraA08t34567Z' => 'bra', 'C03p74380' => 'bna', 'C03p90970' => 'bna', 'C04p10870' => 'bna', 'C05p26240' => 'bna', 'C05p43840' => 'bna', 'C07p17670' => 'bna', 'CAN.G1676.7' => 'can', 'CAN.G21.54' => 'can', 'CAN.G309.88' => 'can', 'CAN.G723.33' => 'can', 'CANSAT25G1314' => 'cansat', 'CANSAT80G1904' => 'cansat', 'CARHR131600' => 'chi', 'CARHR134200' => 'chi', 'Carub.0001s2612' => 'cru', 'Carub.0004s1885' => 'cru', 'Carub.0004s1898' => 'cru', 'Ca_15550_v3' => 'car', 'Ca_15605_v3' => 'car', 'CBR_g19101' => 'cbr', 'Cc06_g03600' => 'ccan', 'Cc08_g09220' => 'ccan', 'Cc10_g08110' => 'ccan', 'Cc10_g08120' => 'ccan', 'CDE04G0110' => 'cde', 'CDE07G1137' => 'cde', 'CDE07G1435' => 'cde', 'Cfa017513' => 'cfa', 'Cfa020696' => 'cfa', 'Ciclev10001397m.g' => 'ccl', 'Ciclev10008306m.g' => 'ccl', 'Ciclev10012036m.g' => 'ccl', 'CiPaw.07G205400' => 'cil', 'CiPaw.09G179500' => 'cil', 'CiPaw.15G151800' => 'cil', 'CiPaw.16G101800' => 'cil', 'ClCG10G020490' => 'cla', 'ClCG11G014880' => 'cla', 'ClCG11G015190' => 'cla', 'COL.COLO4_18673' => 'col', 'COL.COLO4_27071' => 'col', 'COL.COLO4_35343' => 'col', 'Cpa.g.sc286.11' => 'cpa', 'Cpa.g.sc366.2' => 'cpa', 'Cpa.g.sc7.258' => 'cpa', 'CsaV3_3G035620' => 'csa', 'CsaV3_3G048310' => 'csa', 'CsaV3_3G048610' => 'csa', 'CSS0002337' => 'camsi', 'CSS0003996' => 'camsi', 'CSS0005119' => 'camsi', 'CSS0005895' => 'camsi', 'CSS0009292' => 'camsi', 'CSS0022980' => 'camsi', 'CSS0025061' => 'camsi', 'DCAR_004482' => 'dca', 'DCAR_004483' => 'dca', 'DCAR_009285' => 'dca', 'DCAR_012839' => 'dca', 'DCAR_014967' => 'dca', 'Dinv22022' => 'din', 'Dinv30271' => 'din', 'Dinv35715' => 'din', 'Dinv37261' => 'din', 'Dinv44897' => 'din', 'Duzib093G0951' => 'dzi', 'Duzib093G1288' => 'dzi', 'Duzib116G0080' => 'dzi', 'Duzib128G0089' => 'dzi', 'Duzib168G1755' => 'dzi', 'Duzib187G0193' => 'dzi', 'ECA233G3149' => 'eca', 'ECA246G1009' => 'eca', 'ECA248G1901' => 'eca', 'ECA248G3702' => 'eca', 'EL10Ac1g02296' => 'bvu', 'EL10Ac2g04047' => 'bvu', 'EL10Ac7g16505' => 'bvu', 'Eucgr.A01172' => 'egr', 'Eucgr.C00584' => 'egr', 'Eucgr.F00463' => 'egr', 'Eucgr.F02177' => 'egr', 'Eucgr.K03214' => 'egr', 'FAN04G2977' => 'fan', 'FAN05G0747' => 'fan', 'FAN08G1416' => 'fan', 'FAN15G0964' => 'fan', 'FAN18G4139' => 'fan', 'FAN20G0952' => 'fan', 'FAN27G0196' => 'fan', 'FvH4_2g35840' => 'fve', 'FvH4_5g33700' => 'fve', 'FvH4_6g15450' => 'fve', 'Glyma.03G178300' => 'gma', 'Glyma.04G082100' => 'gma', 'Glyma.04G089300' => 'gma', 'Glyma.06G083800' => 'gma', 'Glyma.06G091200' => 'gma', 'Glyma.10G050100' => 'gma', 'Glyma.13G137600' => 'gma', 'Glyma.19G179100' => 'gma', 'Gohir.A01G125200' => 'ghi', 'Gohir.A02G078903' => 'ghi', 'Gohir.A05G047600' => 'ghi', 'Gohir.A06G028900' => 'ghi', 'Gohir.A08G250400' => 'ghi', 'Gohir.A09G151700' => 'ghi', 'Gohir.A13G186050' => 'ghi', 'Gohir.D01G112800' => 'ghi', 'Gohir.D02G086500' => 'ghi', 'Gohir.D05G050100' => 'ghi', 'Gohir.D06G027700' => 'ghi', 'Gohir.D08G271900' => 'ghi', 'Gohir.D09G147400' => 'ghi', 'Gohir.D13G192801' => 'ghi', 'Gorai.002G137600' => 'gra', 'Gorai.004G290300' => 'gra', 'Gorai.005G097300' => 'gra', 'Gorai.006G168500' => 'gra', 'Gorai.009G051500' => 'gra', 'Gorai.010G031000' => 'gra', 'GSVIVG01009245001' => 'vvi', 'GSVIVG01025636001' => 'vvi', 'GSVIVG01035647001' => 'vvi', 'HanXRQChr01g0027461' => 'han', 'HanXRQChr10g0277661' => 'han', 'HanXRQChr12g0380001' => 'han', 'Haze_19003' => 'cav', 'Haze_20635' => 'cav', 'Haze_21874' => 'cav', 'Hma1.2p1_0111F.1_g053940' => 'hma', 'Hma1.2p1_0590F.1_g185020' => 'hma', 'Hma1.2p1_1137F.1_g260780' => 'hma', 'Hma1.2p1_1548F.1_g290000' => 'hma', 'HPP92_001040' => 'vpl', 'HPP92_006747' => 'vpl', 'HPP92_012693' => 'vpl', 'HPP92_023264' => 'vpl', 'HPP92_023302' => 'vpl', 'Hund03405' => 'sun', 'Hund05235' => 'sun', 'Hund28549' => 'sun', 'Hund28550' => 'sun', 'Lalb_Chr01g0018991' => 'lal', 'Lalb_Chr08g0242731' => 'lal', 'Lalb_Chr11g0064751' => 'lal', 'Lalb_Chr23g0269561' => 'lal', 'Lj1g0000395' => 'lja', 'Lj1g0001583' => 'lja', 'Lj1g0007035' => 'lja', 'Lj1g0017307' => 'lja', 'Lj2A108G34' => 'lonja', 'Lj4A81T71' => 'lonja', 'Lj8A588G22' => 'lonja', 'Lsat_1_v5_gn_1_53961' => 'lsa', 'Lsat_1_v5_gn_6_106600' => 'lsa', 'Lsat_1_v5_gn_6_63800' => 'lsa', 'Manes.03G061700' => 'mes', 'Manes.05G186800' => 'mes', 'Manes.08G003900' => 'mes', 'Manes.09G080547' => 'mes', 'Manes.18G054400' => 'mes', 'Mapoly0113s0008' => 'mpo', 'MBI01_g38805_MAGBIO' => 'mbi', 'MBI05_g31761_MAGBIO' => 'mbi', 'MBI16_g20891_MAGBIO' => 'mbi', 'MD04G1103300' => 'mdo', 'MD08G1115800' => 'mdo', 'MD08G1209500' => 'mdo', 'MD12G1123400' => 'mdo', 'MD15G1393400' => 'mdo', 'Medtr3g110142' => 'mtr', 'Medtr3g111060' => 'mtr', 'MELO3C003459.2' => 'cme', 'MELO3C003488.2' => 'cme', 'MELO3C009322.2' => 'cme', 'Migut.A00222' => 'egut', 'Migut.C00410' => 'egut', 'Migut.J00420' => 'egut', 'Migut.L01662' => 'egut', 'MSTRG.10299' => 'ama', 'MSTRG.11706' => 'ama', 'MSTRG.26724' => 'ama', 'MSTRG.9255' => 'ama', 'MSTRG.936' => 'ama', 'Nitab4.5_0000377g0140' => 'nta', 'Nitab4.5_0000406g0010' => 'nta', 'Nitab4.5_0000664g0230' => 'nta', 'Nitab4.5_0000669g0220' => 'nta', 'Nitab4.5_0001567g0170' => 'nta', 'Nitab4.5_0007806g0020' => 'nta', 'Nitab4.5_0008951g0010' => 'nta', 'Nitab4.5_0010450g0010' => 'nta', 'Nn2g10685' => 'nnu', 'Nn2g13011' => 'nnu', 'Nn3g18128' => 'nnu', 'Nn5g29744' => 'nnu', 'Oeu008643.1' => 'oeu', 'Oeu016501.1' => 'oeu', 'Oeu018830.1' => 'oeu', 'Oeu036362.1' => 'oeu', 'Oeu038977.1' => 'oeu', 'Oeu043873.1' => 'oeu', 'Oeu057711.1' => 'oeu', 'Os01g0157700' => 'osa', 'Os01g0675500' => 'osa', 'Os03g0287800' => 'osa', 'Os04g0103100' => 'osa', 'Os05g0123100' => 'osa', 'Os05g0559600' => 'osa', 'Os07g0694400' => 'osa', 'Os10g0205300' => 'osa', 'Peaxi162Scf00005g04210' => 'pax', 'Peaxi162Scf00276g00133' => 'pax', 'Peaxi162Scf00626g00614' => 'pax', 'Peaxi162Scf00822g00007' => 'pax', 'PGR004G0751' => 'pgr', 'PGR031G2185' => 'pgr', 'PGR142G0054' => 'pgr', 'PGSC0003DMG400001769' => 'stu', 'PGSC0003DMG400006379' => 'stu', 'PGSC0003DMG400018584' => 'stu', 'Phvul.001G175200' => 'pvu', 'Phvul.007G164400' => 'pvu', 'Phvul.009G107900' => 'pvu', 'Phvul.009G146400' => 'pvu', 'Potri.002G107300' => 'ptr', 'Potri.006G131000' => 'ptr', 'Potri.006G240200' => 'ptr', 'Potri.016G086400' => 'ptr', 'Potri.018G039901' => 'ptr', 'Pp3c13_8430' => 'ppa', 'Pp3c3_3400' => 'ppa', 'Prupe.1G450500' => 'ppe', 'Prupe.1G541800' => 'ppe', 'Prupe.6G239800' => 'ppe', 'Psat3g044360' => 'psa', 'Psat5g018000' => 'psa', 'Psat5g022680' => 'psa', 'PSO063G4101' => 'pso', 'PSO210G3099' => 'pso', 'PSO210G7611' => 'pso', 'PSO339G6705' => 'pso', 'PSO566G0167' => 'pso', 'PSO675G3623' => 'pso', 'PSO675G4943' => 'pso', 'PSO782G0966' => 'pso', 'QL07p045192' => 'qlo', 'QL12p029438' => 'qlo', 'QL12p040267' => 'qlo', 'RcHm_v2.0_Chr3g0468931' => 'rch', 'RcHm_v2.0_Chr6g0305981' => 'rch', 'RcHm_v2.0_Chr7g0232711' => 'rch', 'Rhsim02G0179500' => 'rsi', 'Rhsim06G0068500' => 'rsi', 'RhsimUnG0115900' => 'rsi', 'Sabra02G0084300' => 'sbr', 'Sabra06G0102900' => 'sbr', 'Sabra16G0092700' => 'sbr', 'SalBow3G0546' => 'sbo', 'SalBow3G0591' => 'sbo', 'SalBow4G1579' => 'sbo', 'SalBow4G2324' => 'sbo', 'SalBow7G1224' => 'sbo', 'SalBow7G2536' => 'sbo', 'Sc02g0001950' => 'sci', 'Sc02g0008360' => 'sci', 'Sc09g0009140' => 'sci', 'Sed0000950' => 'sed', 'Sed0013268' => 'sed', 'Sed0018508' => 'sed', 'Sed0024672' => 'sed', 'SEGI_19182' => 'sgi', 'SEGI_36414' => 'sgi', 'SGA_v2.0_scaffold103G29942' => 'sas', 'SGA_v2.0_scaffold14G07076' => 'sas', 'SMO361G0236' => 'smo', 'Solyc04g076920.3' => 'sly', 'Solyc08g068430.4' => 'sly', 'Solyc09g007420.4' => 'sly', 'Solyc11g071230.2' => 'sly', 'Sopen04g030570' => 'spe', 'Sopen08g022310' => 'spe', 'Sopen11g028920' => 'spe', 'Sp1g23830' => 'spa', 'Sp4g19410' => 'spa', 'TAR369G1044' => 'tar', 'TAR381G0929' => 'tar', 'TAR383G0211' => 'tar', 'TAR623G0354' => 'tar', 'TAR625G1377' => 'tar', 'TAR626G1683' => 'tar', 'TAR628G1492' => 'tar', 'THA.LOC104806494' => 'tha', 'THA.LOC104814773' => 'tha', 'THA.LOC104825809' => 'tha', 'Thecc.05G054900' => 'tca', 'Thecc.08G078500' => 'tca', 'Thecc.09G042600' => 'tca', 'Thhalv10007547m.g' => 'esa', 'Thhalv10016877m.g' => 'esa', 'TPR.G12463' => 'tpr', 'TPR.G1361' => 'tpr', 'TPR.G36975' => 'tpr', 'TWI12G1197' => 'twi', 'TWI34G0162' => 'twi', 'TWI56G0511' => 'twi', 'TWI77G0410' => 'twi', 'unitig_22.g5084' => 'ugi', 'unitig_748.g7502' => 'ugi', 'unitig_88.g27692' => 'ugi', 'vmacro11067' => 'vma', 'vmacro20052' => 'vma', 'vmacro21375' => 'vma', 'vmacro23509' => 'vma', 'VMungo1080G0575' => 'vmu', 'VMungo1309G2040' => 'vmu', 'VMungo1309G3078' => 'vmu', 'VMungo1383G0381' => 'vmu', 'VMungo1383G1466' => 'vmu', 'Zm00001eb013180' => 'zma', 'Zm00001eb036670' => 'zma', 'Zm00001eb069380' => 'zma', 'Zm00001eb089600' => 'zma', 'Zm00001eb112000' => 'zma', 'Zm00001eb123720' => 'zma', 'Zm00001eb156920' => 'zma', 'Zm00001eb241280' => 'zma', 'Zm00001eb254610' => 'zma', 'Zm00001eb265440' => 'zma', 'Zm00001eb295590' => 'zma', 'Zm00001eb332820' => 'zma', 'Zm00001eb343490' => 'zma', 'Zm00001eb355140' => 'zma', 'Zm00001eb399710' => 'zma', 'Zm00001eb418920' => 'zma' ) $gf_id = 'HOM05D001631' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001631' ) $data_identifier = 'HOM05D001631' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 5, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 3, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 8, 'bol' => (int) 4, 'bra' => (int) 3, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 2, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 5, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 5, 'fan' => (int) 7, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 4, 'lal' => (int) 4, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 3, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 5, 'mtr' => (int) 2, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 8, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 3, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 6, 'sci' => (int) 3, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 2, 'tar' => (int) 7, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 3, 'twi' => (int) 4, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 16 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb418920' $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